MemoteReportApp

Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

100.0%

Charge Balance

92.5%

Metabolite Connectivity

100.0%

Unbounded Flux In Default Medium

79.7%

Sub Total

96%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{92.48 + 79.72 + (3 \cdot 100) +}{(5 \cdot 100)} = 96.03$ $(92.48 + 79.72 + (3 * 100) + )/((5 * 100)) = 96.03$

Annotation - Metabolites

Presence of Metabolite Annotation

100.0%

Metabolite Annotations Per Database

pubchem.compound

0.0%

kegg.compound

80.8%

seed.compound

99.5%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

66.8%

biocyc

0.0%

Metabolite Annotation Conformity Per Database

pubchem.compound

0.0%

kegg.compound

100.0%

seed.compound

100.0%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

84.9%

biocyc

0.0%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

62%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{80.77 + 99.52 + 66.77 + 84.94 + (4 \cdot 100) + (16 \cdot 0)}{(24 \cdot 100)} = 62.09$ $(80.77 + 99.52 + 66.77 + 84.94 + (4 * 100) + (16 * 0))/((24 * 100)) = 62.09$

Annotation - Reactions

Presence of Reaction Annotation

100.0%

Reaction Annotations Per Database

rhea

0.0%

kegg.reaction

1.5%

seed.reaction

96.9%

metanetx.reaction

0.0%

bigg.reaction

2.9%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Reaction Annotation Conformity Per Database

rhea

0.0%

kegg.reaction

100.0%

seed.reaction

87.9%

metanetx.reaction

0.0%

bigg.reaction

99.8%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Uniform Reaction Identifier Namespace

100.0%

Sub Total

61%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{1.45 + 96.95 + 2.90 + 87.94 + 99.77 + (3 \cdot 100) + (12 \cdot 0)}{(20 \cdot 100)} = 60.81$ $(1.45 + 96.95 + 2.90 + 87.94 + 99.77 + (3 * 100) + (12 * 0))/((20 * 100)) = 60.81$

Annotation - Genes

Presence of Gene Annotation

100.0%

Gene Annotations Per Database

refseq

100.0%

uniprot

10.7%

ecogene

0.0%

kegg.genes

10.7%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

100.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

100.0%

uniprot

89.3%

ecogene

0.0%

kegg.genes

95.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

50%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{10.71 + 10.71 + 89.29 + 95.00 + (4 \cdot 100) + (13 \cdot 0)}{(21 \cdot 100)} = 50.19$ $(10.71 + 10.71 + 89.29 + 95.00 + (4 * 100) + (13 * 0))/((21 * 100)) = 50.19$

Annotation - SBO Terms

Metabolite General SBO Presence

100.0%

Metabolite SBO:0000247 Presence

100.0%

Reaction General SBO Presence

100.0%

Metabolic Reaction SBO:0000176 Presence

100.0%

Transport Reaction SBO:0000185 Presence

100.0%

Exchange Reaction SBO:0000627 Presence

100.0%

Demand Reaction SBO:0000628 Presence

Skipped

Sink Reactions SBO:0000632 Presence

100.0%

Gene General SBO Presence

100.0%

Gene SBO:0000243 Presence

100.0%

Biomass Reactions SBO:0000629 Presence

100.0%

Sub Total

91%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(10 \cdot 100) + (1 \cdot 0)}{(11 \cdot 100)} = 90.91$ $((10 * 100) + (1 * 0))/((11 * 100)) = 90.91$

Total Score

86%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 96.03) + (1 \cdot 62.09) + (1 \cdot 60.81) + (1 \cdot 50.19) + (2 \cdot 90.91)}{(3 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (2 \cdot 100)} = 86.27$ $((3 * 96.03) + (1 * 62.09) + (1 * 60.81) + (1 * 50.19) + (2 * 90.91))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 86.27$

Total Score

86%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

FBC enabled

Errored

Basic Information

Model Identifier

iCdR700

Total Metabolites

1,243

Total Reactions

1,310

Total Genes

700

Total Compartments

Metabolic Coverage

1.87

Metabolite Information

Unique Metabolites

1,243

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

943

Purely Metabolic Reactions with Constraints

Transport Reactions

174

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

0.36

Reactions With Partially Identical Annotations

0.00

Duplicate Reactions

0.00

Reactions With Identical Genes

0.53

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

183

Fraction of Transport Reactions without GPR

0.39

Enzyme Complexes

Errored

Biomass

Biomass Reactions Identified

Biomass Consistency

biomass

0.02

cellwall_rxn

0.00

cofactor_rxn

0.09

dna_rxn

0.51

lipid_rxn

0.03

peptidoglycan_rxn

2.77

protein_rxn

-0.32

rna_rxn

-0.07

rxn06280_c

0.16

rxn06300_c

0.07

rxn06432_c

0.16

rxn06434_c

0.12

rxn06435_c

0.10

rxn06436_c

0.13

rxn06437_c

0.13

rxn06438_c

0.06

rxn06439_c

0.14

rxn06440_c

0.11

rxn06441_c

0.11

rxn06442_c

0.13

rxn06443_c

0.13

rxn06444_c

0.15

rxn06445_c

0.10

rxn06446_c

0.09

rxn06447_c

0.10

rxn06448_c

0.19

rxn06449_c

0.10

rxn06936_c

0.12

teichoicacid_rxn

1.49

Biomass Production In Default Medium

biomass

41.44

cellwall_rxn

8.29

cofactor_rxn

8.29

dna_rxn

2.07

lipid_rxn

2.07

peptidoglycan_rxn

12.43

protein_rxn

16.58

rna_rxn

10.37

rxn06280_c

3.45

rxn06300_c

4.38

rxn06432_c

2.65

rxn06434_c

5.34

rxn06435_c

1.03

rxn06436_c

6.08

rxn06437_c

1.99

rxn06438_c

5.20

rxn06439_c

1.13

rxn06440_c

8.25

rxn06441_c

7.54

rxn06442_c

7.58

rxn06443_c

2.24

rxn06444_c

3.63

rxn06445_c

2.27

rxn06446_c

5.49

rxn06447_c

4.11

rxn06448_c

0.53

rxn06449_c

5.44

rxn06936_c

4.74

teichoicacid_rxn

0.41

Unrealistic Growth Rate In Default Medium

biomass

true

cellwall_rxn

true

cofactor_rxn

true

dna_rxn

false

lipid_rxn

false

peptidoglycan_rxn

true

protein_rxn

true

rna_rxn

true

rxn06280_c

true

rxn06300_c

true

rxn06432_c

false

rxn06434_c

true

rxn06435_c

false

rxn06436_c

true

rxn06437_c

false

rxn06438_c

true

rxn06439_c

false

rxn06440_c

true

rxn06441_c

true

rxn06442_c

true

rxn06443_c

false

rxn06444_c

true

rxn06445_c

false

rxn06446_c

true

rxn06447_c

true

rxn06448_c

false

rxn06449_c

true

rxn06936_c

true

teichoicacid_rxn

false

Biomass Production In Complete Medium

Using flux balance analysis this test optimizes the model for growth using a complete medium i.e. unconstrained boundary reactions. Any non-zero growth rate is accepted to pass this test. Implementation: Calculate the solution of FBA with the biomass reaction set as objective function and after removing any constraints from all boundary reactions.

biomass

183.67

cellwall_rxn

36.73

cofactor_rxn

36.73

dna_rxn

9.18

lipid_rxn

9.18

peptidoglycan_rxn

55.10

protein_rxn

73.47

rna_rxn

45.96

rxn06280_c

15.28

rxn06300_c

19.40

rxn06432_c

11.75

rxn06434_c

23.66

rxn06435_c

4.55

rxn06436_c

26.96

rxn06437_c

8.82

rxn06438_c

23.07

rxn06439_c

5.00

rxn06440_c

36.59

rxn06441_c

33.43

rxn06442_c

33.57

rxn06443_c

9.92

rxn06444_c

16.09

rxn06445_c

10.06

rxn06446_c

24.32

rxn06447_c

18.22

rxn06448_c

2.35

rxn06449_c

24.10

rxn06936_c

21.01

teichoicacid_rxn

1.84

Blocked Biomass Precursors In Default Medium

biomass

cellwall_rxn

cofactor_rxn

dna_rxn

lipid_rxn

peptidoglycan_rxn

protein_rxn

rna_rxn

rxn06280_c

rxn06300_c

rxn06432_c

rxn06434_c

rxn06435_c

rxn06436_c

rxn06437_c

rxn06438_c

rxn06439_c

rxn06440_c

rxn06441_c

rxn06442_c

rxn06443_c

rxn06444_c

rxn06445_c

rxn06446_c

rxn06447_c

rxn06448_c

rxn06449_c

rxn06936_c

teichoicacid_rxn

Blocked Biomass Precursors In Complete Medium

biomass

cellwall_rxn

cofactor_rxn

dna_rxn

lipid_rxn

peptidoglycan_rxn

protein_rxn

rna_rxn

rxn06280_c

rxn06300_c

rxn06432_c

rxn06434_c

rxn06435_c

rxn06436_c

rxn06437_c

rxn06438_c

rxn06439_c

rxn06440_c

rxn06441_c

rxn06442_c

rxn06443_c

rxn06444_c

rxn06445_c

rxn06446_c

rxn06447_c

rxn06448_c

rxn06449_c

rxn06936_c

teichoicacid_rxn

Ratio of Direct Metabolites in Biomass Reaction

biomass

0.00

cellwall_rxn

0.00

cofactor_rxn

0.29

dna_rxn

0.00

lipid_rxn

0.00

peptidoglycan_rxn

0.00

protein_rxn

0.00

rna_rxn

0.00

rxn06280_c

0.00

rxn06300_c

0.00

rxn06432_c

0.00

rxn06434_c

0.00

rxn06435_c

0.00

rxn06436_c

0.00

rxn06437_c

0.00

rxn06438_c

0.00

rxn06439_c

0.00

rxn06440_c

0.00

rxn06441_c

0.00

rxn06442_c

0.00

rxn06443_c

0.00

rxn06444_c

0.00

rxn06445_c

0.00

rxn06446_c

0.00

rxn06447_c

0.00

rxn06448_c

0.00

rxn06449_c

0.00

rxn06936_c

0.00

teichoicacid_rxn

0.00

Number of Missing Essential Biomass Precursors

biomass

cellwall_rxn

cofactor_rxn

dna_rxn

lipid_rxn

peptidoglycan_rxn

protein_rxn

rna_rxn

rxn06280_c

rxn06300_c

rxn06432_c

rxn06434_c

rxn06435_c

rxn06436_c

rxn06437_c

rxn06438_c

rxn06439_c

rxn06440_c

rxn06441_c

rxn06442_c

rxn06443_c

rxn06444_c

rxn06445_c

rxn06446_c

rxn06447_c

rxn06448_c

rxn06449_c

rxn06936_c

teichoicacid_rxn

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

biomass

false

cellwall_rxn

false

cofactor_rxn

false

dna_rxn

false

lipid_rxn

false

peptidoglycan_rxn

false

protein_rxn

false

rna_rxn

false

rxn06280_c

false

rxn06300_c

false

rxn06432_c

false

rxn06434_c

false

rxn06435_c

false

rxn06436_c

false

rxn06437_c

false

rxn06438_c

false

rxn06439_c

false

rxn06440_c

false

rxn06441_c

false

rxn06442_c

false

rxn06443_c

false

rxn06444_c

false

rxn06445_c

false

rxn06446_c

false

rxn06447_c

false

rxn06448_c

false

rxn06449_c

false

rxn06936_c

false

teichoicacid_rxn

false

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

456

Orphan Metabolites

Dead-end Metabolites

Stoichiometrically Balanced Cycles

168

Metabolite Production In Complete Medium

506

Metabolite Consumption In Complete Medium

537

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

193

Rank

1050

Degrees Of Freedom

260

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.10

Platform Linux

Memote Version 0.10.2

Package Versions